A decade of riboswitches

Cell

Volumn 152, Issue 1-2, 2013, Pages 17-24

  Serganov, Alexander ^a   Nudler, Evgeny ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENE; GENETIC ANALYSIS; METABOLITE; MOLECULAR RECOGNITION; MOLECULAR SENSOR; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; RIBOSWITCH; RNA DEGRADATION; RNA SPLICING; RNA STABILITY; RNA TRANSLATION; TRANSCRIPTION REGULATION;

EID: 84872543206     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2012.12.024     Document Type: Review

References (86)

1. J.L. Baker, N. Sudarsan, Z. Weinberg, A. Roth, R.B. Stockbridge, and R.R. Breaker Widespread genetic switches and toxicity resistance proteins for fluoride Science 335 2012 233 235
2. R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415 (Pubitemid 39551677)
3. S. Bocobza, A. Adato, T. Mandel, M. Shapira, E. Nudler, and A. Aharoni Riboswitch-dependent gene regulation and its evolution in the plant kingdom Genes Dev. 21 2007 2874 2879 (Pubitemid 350133436)
4. R.R. Breaker Riboswitches and the RNA world R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World 2006 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY 89 108
5. R.R. Breaker Prospects for riboswitch discovery and analysis Mol. Cell 43 2011 867 879
6. E.B. Butler, Y. Xiong, J. Wang, and S.A. Strobel Structural basis of cooperative ligand binding by the glycine riboswitch Chem. Biol. 18 2011 293 298
7. M.T. Cheah, A. Wachter, N. Sudarsan, and R.R. Breaker Control of alternative RNA splicing and gene expression by eukaryotic riboswitches Nature 447 2007 497 500 (Pubitemid 46816734)
8. A.G.Y. Chen, N. Sudarsan, and R.R. Breaker Mechanism for gene control by a natural allosteric group I ribozyme RNA 17 2011 1967 1972
9. J.C. Cochrane, S.V. Lipchock, and S.A. Strobel Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Chem. Biol. 14 2007 97 105 (Pubitemid 46124067)
10. J.A. Collins, I. Irnov, S. Baker, and W.C. Winkler Mechanism of mRNA destabilization by the glmS ribozyme Genes Dev. 21 2007 3356 3368 (Pubitemid 350277761)
11. K.A. Corbino, J.E. Barrick, J. Lim, R. Welz, B.J. Tucker, I. Puskarz, M. Mandal, N.D. Rudnick, and R.R. Breaker Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria Genome Biol. 6 2005 R70
12. M.T. Croft, M. Moulin, M.E. Webb, and A.G. Smith Thiamine biosynthesis in algae is regulated by riboswitches Proc. Natl. Acad. Sci. USA 104 2007 20770 20775
13. (2+) Cell 125 2006 71 84
14. C.E. Dann III, C.A. Wakeman, C.L. Sieling, S.C. Baker, I. Irnov, and W.C. Winkler Structure and mechanism of a metal-sensing regulatory RNA Cell 130 2007 878 892 (Pubitemid 47332567)
15. N. Dixon, J.N. Duncan, T. Geerlings, M.S. Dunstan, J.E. McCarthy, D. Leys, and J. Micklefield Reengineering orthogonally selective riboswitches Proc. Natl. Acad. Sci. USA 107 2010 2830 2835
16. N. Dixon, C.J. Robinson, T. Geerlings, J.N. Duncan, S.P. Drummond, and J. Micklefield Orthogonal riboswitches for tuneable coexpression in bacteria Angew. Chem. Int. Ed. Engl. 51 2012 3620 3624
17. T.E. Edwards, and A.R. Ferré-D'Amaré Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition Structure 14 2006 1459 1468 (Pubitemid 44331619)
18. A.D. Ellington, and J.W. Szostak In vitro selection of RNA molecules that bind specific ligands Nature 346 1990 818 822
19. V. Epshtein, A.S. Mironov, and E. Nudler The riboswitch-mediated control of sulfur metabolism in bacteria Proc. Natl. Acad. Sci. USA 100 2003 5052 5056 (Pubitemid 36542656)
20. K.A. Fox, A. Ramesh, J.E. Stearns, A. Bourgogne, A. Reyes-Jara, W.C. Winkler, and D.A. Garsin Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis Proc. Natl. Acad. Sci. USA 106 2009 4435 4440
21. MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase Nat. Struct. Mol. Biol. 13 2006 226 233 (Pubitemid 43348508)
22. A.D. Garst, A. Héroux, R.P. Rambo, and R.T. Batey Crystal structure of the lysine riboswitch regulatory mRNA element J. Biol. Chem. 283 2008 22347 22351
23. M.S. Gelfand, A.A. Mironov, J. Jomantas, Y.I. Kozlov, and D.A. Perumov A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes Trends Genet. 15 1999 439 442 (Pubitemid 29507036)
24. W. Gilbert Origin of life: the RNA world Nature 319 1986 618
25. S.D. Gilbert, R.P. Rambo, D. Van Tyne, and R.T. Batey Structure of the SAM-II riboswitch bound to S-adenosylmethionine Nat. Struct. Mol. Biol. 15 2008 177 182 (Pubitemid 351207508)
26. J. Gralla, J.A. Steitz, and D.M. Crothers Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA Nature 248 1974 204 208
27. F.J. Grundy, and T.M. Henkin tRNA as a positive regulator of transcription antitermination in B. subtilis Cell 74 1993 475 482 (Pubitemid 23244613)
28. A. Haller, U. Rieder, M. Aigner, S.C. Blanchard, and R. Micura Conformational capture of the SAM-II riboswitch Nat. Chem. Biol. 7 2011 393 400
29. K. Hollands, S. Proshkin, S. Sklyarova, V. Epshtein, A. Mironov, E. Nudler, and E.A. Groisman Riboswitch control of Rho-dependent transcription termination Proc. Natl. Acad. Sci. USA 109 2012 5376 5381
30. L. Huang, A. Serganov, and D.J. Patel Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch Mol. Cell 40 2010 774 786
31. L. Huang, S. Ishibe-Murakami, D.J. Patel, and A. Serganov Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch Proc. Natl. Acad. Sci. USA 108 2011 14801 14806
32. L. Jaeger, E.J. Verzemnieks, and C. Geary The UA-handle: a versatile submotif in stable RNA architectures Nucleic Acids Res. 37 2009 215 230
33. J.E. Johnson Jr.; F.E. Reyes, J.T. Polaski, and R.T. Batey B12 cofactors directly stabilize an mRNA regulatory switch Nature 492 2012 133 137
34. W. Kladwang, F.C. Chou, and R. Das Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches J. Am. Chem. Soc. 134 2012 1404 1407
35. D.J. Klein, and A.R. Ferré-D'Amaré Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Science 313 2006 1752 1756 (Pubitemid 44454144)
36. M. Kwon, and S.A. Strobel Chemical basis of glycine riboswitch cooperativity RNA 14 2008 25 34
37. E.-J. Lee, and E.A. Groisman Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA Nature 486 2012 271 275
38. E.R. Lee, J.L. Baker, Z. Weinberg, N. Sudarsan, and R.R. Breaker An allosteric self-splicing ribozyme triggered by a bacterial second messenger Science 329 2010 845 848
39. J.F. Lemay, G. Desnoyers, S. Blouin, B. Heppell, L. Bastet, P. St-Pierre, E. Massé, and D.A. Lafontaine Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms PLoS Genet. 7 2011 e1001278
40. D.M. Lilley, and F. Eckstein Ribozymes and RNA catalysis: introduction and primer D.M. Lilley, F. Eckstein, Ribozymes and RNA Catalysis 2008 The Royal Society of Chemistry Cambridge 1 8
41. E. Loh, O. Dussurget, J. Gripenland, K. Vaitkevicius, T. Tiensuu, P. Mandin, F. Repoila, C. Buchrieser, P. Cossart, and J. Johansson A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes Cell 139 2009 770 779
42. MK) riboswitch reveal the SAM-dependent translation inhibition mechanism Nat. Struct. Mol. Biol. 15 2008 1076 1083
43. M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, and R.R. Breaker A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science 306 2004 275 279 (Pubitemid 39336872)
44. B.A. McDaniel, F.J. Grundy, I. Artsimovitch, and T.M. Henkin Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA Proc. Natl. Acad. Sci. USA 100 2003 3083 3088 (Pubitemid 36356543)
45. J. Miranda-Ríos, M. Navarro, and M. Soberón A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria Proc. Natl. Acad. Sci. USA 98 2001 9736 9741 (Pubitemid 32769373)
46. A.S. Mironov, I. Gusarov, R. Rafikov, L.E. Lopez, K. Shatalin, R.A. Kreneva, D.A. Perumov, and E. Nudler Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria Cell 111 2002 747 756 (Pubitemid 35446317)
47. R.K. Montange, and R.T. Batey Structure of the S-adenosylmethionine riboswitch regulatory mRNA element Nature 441 2006 1172 1175 (Pubitemid 43990740)
48. J. Mulhbacher, E. Brouillette, M. Allard, L.C. Fortier, F. Malouin, and D.A. Lafontaine Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways PLoS Pathog. 6 2010 e1000865
49. A. Nahvi, N. Sudarsan, M.S. Ebert, X. Zou, K.L. Brown, and R.R. Breaker Genetic control by a metabolite binding mRNA Chem. Biol. 9 2002 1043 1049 (Pubitemid 35273725)
50. G. Nechooshtan, M. Elgrably-Weiss, A. Sheaffer, E. Westhof, and S. Altuvia A pH-responsive riboregulator Genes Dev. 23 2009 2650 2662
51. X. Nou, and R.J. Kadner Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli J. Bacteriol. 180 1998 6719 6728
52. X. Nou, and R.J. Kadner Adenosylcobalamin inhibits ribosome binding to btuB RNA Proc. Natl. Acad. Sci. USA 97 2000 7190 7195 (Pubitemid 30431439)
53. J.B. Perkins, and J. Pero Biosynthesis of riboflavin, biotin, folic acid, and cobalamin A.L. Sonenshein, J.A. Hoch, R. Losick, Bacillus subtillis and Its Closest Relatives: From Genes to Cells 2002 ASM Press Washington 271 286
54. A. Peselis, and A. Serganov Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch Nat. Struct. Mol. Biol. 19 2012 1182 1184
55. O. Pikovskaya, A. Polonskaia, D.J. Patel, and A. Serganov Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch Nat. Chem. Biol. 7 2011 748 755
56. S. Ravnum, and D.I. Andersson An adenosyl-cobalamin (coenzyme-B12)- repressed translational enhancer in the cob mRNA of Salmonella typhimurium Mol. Microbiol. 39 2001 1585 1594 (Pubitemid 32269755)
57. P.S. Ray, J. Jia, P. Yao, M. Majumder, M. Hatzoglou, and P.L. Fox A stress-responsive RNA switch regulates VEGFA expression Nature 457 2009 915 919
58. 2+ ions and phosphates in a fluoride riboswitch Nature 486 2012 85 89
59. D.L. Robertson, and G.F. Joyce Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA Nature 344 1990 467 468
60. A. Serganov, Y.R. Yuan, O. Pikovskaya, A. Polonskaia, L. Malinina, A.T. Phan, C. Hobartner, R. Micura, R.R. Breaker, and D.J. Patel Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs Chem. Biol. 11 2004 1729 1741 (Pubitemid 39651306)
61. A. Serganov, A. Polonskaia, A.T. Phan, R.R. Breaker, and D.J. Patel Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature 441 2006 1167 1171 (Pubitemid 43990739)
62. A. Serganov, L. Huang, and D.J. Patel Structural insights into amino acid binding and gene control by a lysine riboswitch Nature 455 2008 1263 1267
63. A. Serganov, L. Huang, and D.J. Patel Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Nature 458 2009 233 237
64. E.M. Sherman, J. Esquiaqui, G. Elsayed, and J.D. Ye An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches RNA 18 2012 496 507
65. J. Sinha, S.J. Reyes, and J.P. Gallivan Reprogramming bacteria to seek and destroy an herbicide Nat. Chem. Biol. 6 2010 464 470
66. C.D. Stoddard, R.K. Montange, S.P. Hennelly, R.P. Rambo, K.Y. Sanbonmatsu, and R.T. Batey Free state conformational sampling of the SAM-I riboswitch aptamer domain Structure 18 2010 787 797
67. G.D. Stormo, and Y. Ji Do mRNAs act as direct sensors of small molecules to control their expression? Proc. Natl. Acad. Sci. USA 98 2001 9465 9467 (Pubitemid 32769323)
68. N. Sudarsan, M.C. Hammond, K.F. Block, R. Welz, J.E. Barrick, A. Roth, and R.R. Breaker Tandem riboswitch architectures exhibit complex gene control functions Science 314 2006 300 304 (Pubitemid 44571975)
69. N. Sudarsan, E.R. Lee, Z. Weinberg, R.H. Moy, J.N. Kim, K.H. Link, and R.R. Breaker Riboswitches in eubacteria sense the second messenger cyclic di-GMP Science 321 2008 411 413 (Pubitemid 352029978)
70. B. Suess, B. Fink, C. Berens, R. Stentz, and W. Hillen A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo Nucleic Acids Res. 32 2004 1610 1614 (Pubitemid 38854758)
71. S. Thore, M. Leibundgut, and N. Ban Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand Science 312 2006 1208 1211 (Pubitemid 43801145)
72. J. Tomsic, B.A. McDaniel, F.J. Grundy, and T.M. Henkin Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in Bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro J. Bacteriol. 190 2008 823 833 (Pubitemid 351170925)
73. J.J. Trausch, P. Ceres, F.E. Reyes, and R.T. Batey The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer Structure 19 2011 1413 1423
74. C. Tuerk, and L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
75. A. Verhounig, D. Karcher, and R. Bock Inducible gene expression from the plastid genome by a synthetic riboswitch Proc. Natl. Acad. Sci. USA 107 2010 6204 6209
76. M.M.K. Vu, N.E. Jameson, S.J. Masuda, D. Lin, R. Larralde-Ridaura, and A. Lupták Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX Chem. Biol. 19 2012 1247 1254
77. A. Wachter, M. Tunc-Ozdemir, B.C. Grove, P.J. Green, D.K. Shintani, and R.R. Breaker Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs Plant Cell 19 2007 3437 3450
78. P.Y. Watson, and M.J. Fedor The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo Nat. Struct. Mol. Biol. 18 2011 359 363
79. P.Y. Watson, and M.J. Fedor The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis Nat. Chem. Biol. 8 2012 963 965
80. Z. Weinberg, J.E. Barrick, Z. Yao, A. Roth, J.N. Kim, J. Gore, J.X. Wang, E.R. Lee, K.F. Block, and N. Sudarsan Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline Nucleic Acids Res. 35 2007 4809 4819 (Pubitemid 47250352)
81. Z. Weinberg, J.X. Wang, J. Bogue, J. Yang, K. Corbino, R.H. Moy, and R.R. Breaker Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes Genome Biol. 11 2010 R31
82. J.K. Wickiser, W.C. Winkler, R.R. Breaker, and D.M. Crothers The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch Mol. Cell 18 2005 49 60 (Pubitemid 40444647)
83. W. Winkler, A. Nahvi, and R.R. Breaker Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419 2002 952 956 (Pubitemid 35339632)
84. W.C. Winkler, A. Nahvi, N. Sudarsan, J.E. Barrick, and R.R. Breaker An mRNA structure that controls gene expression by binding S-adenosylmethionine Nat. Struct. Biol. 10 2003 701 707 (Pubitemid 37052407)
85. W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 2004 281 286 (Pubitemid 38418792)
86. C. Yanofsky Attenuation in the control of expression of bacterial operons Nature 289 1981 751 758 (Pubitemid 11150411)